Yes you should've been ahead of anyone getting a comp upgrade. This is unfortunately still a systemic problem with agents not applying the proper coding to the PNR when a pax is using a SWU for domestic flights. As mentioned, you should've had a UP2A code but most likely only had UP3D since the system did not see the SWU due to the missing and/or incorrect coding.

Definitely send an email to cust service and ask for an investigation since this is happening most of the time. This needs to get fixed.